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DNA study gives insight into the evolution of food crops, other flowering plants

The Amborella female flower. Image: Sangtae Kim

Barbara Kennedy

January 7, 2014

Publication of the newly sequenced genome of the Amborella plant has shed new light on a major event in the history of life on Earth -- the origin of all major food crops and all other flowering plants. The research addresses the question of why flowers suddenly proliferated on Earth millions of years ago.

A paper by the Amborella Genome Sequencing Project, which includes Penn State scientists and students, was published by the journal Science in the Dec. 20 issue. The paper is among three on different research areas related to the Amborella genome that appear in the issue, along with a "Perspective" commentary by the journal.

Claude dePamphilis, professor of biology at Penn State, the overall principal investigator for the project and the corresponding author for the paper, is the only scientist who is a coauthor of all three papers.

Amborella (Amborella trichopoda) is unique as the sole survivor of an ancient evolutionary lineage that traces back to the last common ancestor of all flowering plants. The plant is a small tree found only on the main island of New Caledonia in the South Pacific. An effort to decipher the Amborella genome -- led by scientists at Penn State, the University at Buffalo, the University of Florida, the University of Georgia and the University of California-Riverside -- is uncovering evidence for the evolutionary processes that paved the way for the amazing diversity of the more than 300,000 flowering plant species on Earth today.

This unique heritage gives Amborella a special role in the study of flowering plants. The scientists who sequenced the Amborella genome said it provides conclusive evidence that the ancestor of all flowering plants, including Amborella, evolved following a "genome doubling event" that occurred about 200 million years ago. Some duplicated genes were lost over time but others took on new functions, including contributions to the development of floral organs.

"Genome doubling may offer an explanation for the apparently abrupt proliferation of new species of flowering plants in fossil records dating to the Cretaceous period," dePamphilis said. "Generations of scientists have worked to solve this puzzle, known as Darwin's "abominable mystery."

Comparative analyses of the Amborella genome already are providing scientists with a new perspective on the genetic origins of important traits in all flowering plants -- including all major food-crop species.

Joshua Der, a research associate in the dePamphilis lab and the project manager of Amborella Genome Project, said "We estimate that at least 14,000 protein-coding genes existed in the last common ancestor of all flowering plants. Many of these genes are unique to flowering plants, and many are known to be important for producing the flower as well as other structures and other processes specific to flowering plants."

The scientists indicated that this research provides the first global insight into how flowering plants are genetically different from all other plants on Earth, and it gives new clues about how seed plants are genetically different from non-seed plants.

In addition to its usefulness in studies of the evolution of flowering plants, the Amborella genome sequence offers insights into the history and conservation of Amborella populations. There are only 18 known populations of this special angiosperm in the mountainous regions of New Caledonia. The complete genome sequence of Amborella has been deposited in Genbank -- the U.S. National Institutes of Health database of publicly available gene sequences -- and also is available in the Amborella Genome Database (www.Amborella.org).

In addition to dePamphilis and Der, Penn State faculty members who participated in the research include Hong Ma, professor of biology and a co-principal investigator of the project, who performed studies of the evolution of gene families; Stephan C. Schuster, professor of biochemistry and molecular biology, in whose lab the Amborella genome and transcriptome sequencing were performed; Naomi Altman, professor of statistics, who contributed statistical analyses; and Michael Axtell, associate professor, biology, who performed analyses to annotate and study the small RNA genes in Amborella, revealing new information about some common and also very unusual microRNAs.

Other Penn State contributors to the research include Yuannian Jiao, who earned his doctorate degree in plant biology and was a postdoctoral associate in dePamphilis lab before moving recently to a postdoctoral position at the University of Georgia; graduate students Eric Wafula and Saima Shahid; undergraduate student Nina P. Farrell; technicians Paula Ralph, Lynn Tomsho and Riva A. Bruenn; and Hongzhi Kong, who was a postdoctoral associate in the Ma and dePamphilis labs before becoming a professor at the Chinese Academy of Sciences in Beijing.

In addition to researchers at Penn State, the paper's authors include scientists from the University at Buffalo, the University of Florida, the University of Georgia and the University of California-Riverside, and from other universities in the United States, Canada, Mexico, China, Korea, Taiwan, Singapore, Germany, Italy, Denmark, France and New Caledonia in the South Pacific.

The National Science Foundation's Plant Genome Research Program funded this work.